Citations are links, so where is the problem?

Citations are a fundamental concept of scholarly works. Unfortunately they are also difficult to do. Traditional writing tools such as Microsoft Word can’t really handle them in a way that is appropriate for a scientific manuscript, and that is why we have reference managers such as Endnote, Zotero or Mendeley. And the lack of this functionality is a major reason that Google Docs and other online collaborative writing tools haven’t become popular for writing scholarly works.

1958 Edsel Citation

1958 Edsel Citation by Roadsidepictures, on Flickr.

Using citations is hard for paper authors. The process is still complicated when using a reference manager, and it remains one of the more time consuming aspects of writing a manuscript. The main reason is that something always seems to go wrong with the formatting of the bibliography, but there are also issues of wrong or duplicate citations (including citation mutations), correct citation styles, etc. I can’t comment on how well BibTeX integrates citation management into LaTeX, but the main issue seems to be that citations usually are not one of the core functions of the writing tool.

WordPress and reference managers
The blogging platform WordPress could become an excellent authoring platform for scientific papers. But to become successful, WordPress has to handle scholarly citations, and not just with copy and paste. Carl Boettinger has written about doing citations in WordPress ealier this week and there is also an ongoing FriendFeed discussion. I have also looked at the available plugins, in particular papercite (based on bib2html) which uses the BibTex format and is giving me some problems. I can’t get the CrossRef Citation plugin to work (SyntaxError: Parse error) and the Mendeley Plugin is displaying bibliographies, rather than inserting citations. There is currently probably no easy solution to cite scholarly works in WordPress and I don’t think that creating a WordPress Plugin for one of the reference managers is the right approach.

Citations are links
If we think about it, citations are nothing more than specialized links that contain additional information and formatting. And the references section is a list of footnotes. Links are a genuine part of WordPress, and this system should therefore also be used when writing scholarly works with WordPress. A Citation Plugin should extend this system, and solve these issues:

  • WordPress isn’t very smart about footnotes. I use the WP-Footnotes Plugin, but we need additional functionality: avoid duplicates, formatting options of in-text citations (e.g. range of citations or author-year) and sorting of footnotes by occurence or name.
  • The tool to create links in articles is not really integrated with the WordPress Links system (in contrast to images, where you have access to the media gallery when inserting an image).

Both of  these issues can be solved, especially since they are not specific to scholarly works and could be tackled by thousands of WordPress developers out there.

We don’t want to use WordPress as a reference manager, as there are already many tools out there that can do this job much better. We rather want reference manager integration with WordPress, and the easiest way to do this would be an automatic synchronization with the WordPress Links database. We can already do this with the social bookmarking tool delicious (I use DeliciousLinkSync), so it shouldn’t be difficult to do this with the social bookmarking tools for scientists such as CiteULike (you can sync CiteULike with delicious, a workaround I currently use), Connotea or BibSonomy.

Links are powerful
Using the WordPress Links system makes it very easy to extend the core functionality, and many interesting tools are already out there. A good example is the Broken Link Checker. The Plugin can regularly check the links in your blog posts, but could also be used to check DOIs for references in a semi-automated way. The Broken Link Checker found 30 broken links in the Blogging Beyond the PDF sample article (all my fault), and automatically changed the display style for them.

And there is so much more that can be done with links. I am particularly interested in adding meaning to links using the Citation Typing Ontology (CiTO). And I want to be able to cite specific parts of an article. Dave Winer has introduced paragraph-level permalinks to blogs, and I can do this on WordPress using the WinerLinks Plugin. The broken links in my Blogging Beyond the PDF sample article are all internal links, and I can now use WinerLinks to fix them. An example where I have already done this is the reference to Table S8 in this paragraph.

Update on 12/11/10: I’ve installed the Anotar Plugin by Peter Sefton that adds paragraph-level commenting.

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19 Responses to Citations are links, so where is the problem?

  1. Hi, Martin.

    The CiTO link in the post seems to be broken …

  2. Akshat Rathi says:

    This is a great idea. I think you are right about wordpress having the potential to be a great collaborative tool. I wonder though how wordpress can offline working. There should be a mechanism to store locally. Also, there should be a method by which wordpress articles can be emailed. I can see how this can transcend the PDF.

  3. Martin Fenner says:

    Frank, sorry for the broken CiTO link, it is fixed now (removed an extra period at the end). Maybe I should ask to install Broken Link Checker for PLoS Blogs.

    I haven’t yet had time to study how Citation Style Language could help with citations in WordPress.

    Akshat, there are a number of tools to use WordPress offline, on the Mac I use MarsEdit.

  4. Instead of using bib2html I would recommend using JabRef and its HTML export functionality. http://jabref.sourceforge.net
    In short, the only thing you need is a template file and that works pretty generically. Actually, I have created the very first template mechanism in JabRef, which has quite advanced since then, so let me know if you need any help.

  5. Carl says:

    Thanks for the mention and pointers to some more useful plugins. Wonder what’s up with the papercite install? took me a bit of fiddling. Nice to be able to add the links by using the article key instead of adding them manually.

  6. Martin Fenner says:

    Joerg, thanks for mentioning HTML export in JabRef. You can do something similar with most reference managers, and that is how I currently do citations in blog posts. But I would very much prefer to do citations as WordPress links.

    Carl, I haven’t yet fixed my papercite install. I have so far only tried linking to my CiteULike bibliography instead of uploading the BibTeX file to the WordPress server.

  7. Martin, Thanks for another great post and the rich links that you have provided.

    However I like to point out that WizFolio’s WizCite is cross-platform, word processor agnostic citation generator and will work seamlessly with WordPress. Yes we generate citations using links.

    WizCite will work not only with desktop word processor like MS Word (Window) and OpenOffice (Mac and Windows) but also with web based word process like Google Docs (version prior July 2010) and Zoho Writer. You can see a YouTube demo here http://goo.gl/SvGiO .

    One can look at WordPress as a web based “word processor.” WizCite is a full fledge citation engine that will work with WordPress, as well as Google Sites. Instruction to install WizCite for WordPress is the same as for Google Docs. http://goo.gl/zATuW

    Interested to hear if WizCite is meeting most of your expectations of a citation generator for WordPress. If it does, then we hope this is a small step “beyond PDF.”

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  10. Mr. Gunn says:

    Thanks for presenting the problem so clearly, Martin. I’ve thought about this myself and I always find myself wanting links in papers. In fact, the whole style we have (short mentions in the text, a bibliography at the end) is designed to fit the print idiom. You’re not limited to one page or a two-dimensional canvas when writing for the web, so there’s no need to force people to click or scroll away from where they were reading to check out the paper you were citing, nor is there any need to make them parse a inscrutable citation format and further promote citation mutation. Most papers have links these days (DOIs, etc) so you could put those inline and fill the link metatags with all the information you’d need.

    That’s what I’d like to see, not some shovelware porting of the print metaphor to online writing.

  11. Martin Fenner says:

    William, I completely agree, but I don’t know how to do the details. How should we cite a paper using an inline link? Author-year in parentheses, using the paper title, something else?

  12. Bruce D'Arcus says:

    There is currently probably no easy solution to cite scholarly works in WordPress and I don’t think that creating a WordPress Plugin for one of the reference managers is the right approach.

    I agree.

    The problem is that formatting in references managers is based on a very tight coupling of users application data and formatted output. This is a broken model, and has all kinds of negative consequences.

    On the CSL end, Zotero recently announced a web service that can spit out formatted references based on CSL styles. So what if we just standardized the CSL API, and allowed little plug-ins in WordPress, Drupal, Google Docs, etc. hook up to those? The only current problem is that this service is still based on the limitation I note above: input is a list of Zotero items. That’s not good enough.

  13. Martin Fenner says:

    Bruce,

    I agree and hope that we will see reference management for WordPress in 2011. Ideally this should be a two-part solution: a) a modified links database that hold relevant reference metadata and can be synced with CiteULike, Zotero, Mendeley or Endnote Web, and b) a plugin that puts the citations into the WordPress article, probably using your CSL.

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  16. whofero says:

    Fascinating post

  17. Anita says:

    Couple of problems that I would like to bring up that have not been dealt with:
    1. I would like to cite data elements inside of papers, which have no current live links (Bob in 2010 showed X in this figure)
    2. I would also like to link data that may not be part of any publication and citing the entirety of MGI’s 2000000 should not be the way to do this
    3. What if MGI or another database that I have cited has a funding downturn? The data should still be maintained somewhere…
    Just some food for thought

  18. Anita, the Winerlinks plugin that I mentioned addresses #1. I agree that data citation is still a big problem. Some of these questions will be addressed in a Data Citation Principles workshop in May.

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